I doubt that recapping the Acquisition board will help much. While it is true that Tek had serious problems with caps leaking on early TDSXXX units like the TDS520A, 544A, 644A, and the like, the newer units didn't really have that many issues. I assume this is because the quality of the caps improved by the time the newer units came along.
Do you get this error during the self test or during SPC calibration? The reason I ask is that this error is common when running SPC - this is usually fixed by replacing the relays of the attenuator hybrid. I haven't seen this during diagnostics, but I suppose it is still possible.
One thing that would be helpful is to attach a console port to the main board when you boot up and when running diags and/or SPC. This will spew out errors when it encounters them and that is usually a good clue. At the very list it may help to determine which channel is having issues.